The parents will hand leaflets to people visiting the Chelsea and Westminster Hospital in west London to explain how the closure of the vitamin B12 clinic is affecting hundreds of patients, mainly the young.
The children suffer from conditions including severe brain disorders and seizures thought to be linked to a deficiency of the vitamin B12.
Frank Redmond, 45, from London, helped plan the protest because he said the trust's decision had ended tests on his four-year-old daughter Tess, who suffers fits, before a diagnosis had been reached. Mr Redmond said he and three other parents had also reported the closure to the Health Service Ombudsman for investigation.
Dr Ray Bhatt, who ran the unit, one of only four in the world, is no longer able to offer specialist advice and testing because of the dispute over his and the unit's future.
The hospital has said it cannot renew Dr Bhatt's contract until the unit's work has been submitted for peer review and it can guarantee the safety of its patients.
However, correspondence last month from another expert supported Dr Bhatt. Professor Victor Herbert, of the Mount Sinai School of Medicine, New York, said the doctor was regarded by as an "outstanding researcher and physician".Reuse content